To evaluate residual root filling material following removal of three newly developed root canal sealers used with a matched-taper single-cone root filling technique and to compare the efficacy of ProTaper Universal rotary retreatment instruments with that of a conventional manual technique. The canals of 120 palatal roots in maxillary molar teeth were instrumented with EndoWave nickel-titanium rotary instruments and filled using Hybrid Root SEAL, EndoSequence BC Sealer, Activ GP system or AH Plus with matched-taper single gutta-percha cones. The root fillings were then removed with ProTaper Universal retreatment rotary instruments or a manual technique. Buccolingual and proximal digital radiographs of the roots were exposed to determine the area of remaining filling material in the coronal, middle and apical thirds. The area percentages of remaining filling material in each third and total canal area were calculated. Data were analysed statistically with Kruskal-Wallis and Mann-Whitney U-tests. The level of significance was set at P<0.05. Irrespective of the sealer type and retreatment technique, filling material could not be removed completely from the root canals. Significantly, more remaining filling material was observed in the apical third (P<0.05). When comparing the sealers, the only significant difference was detected between AH Plus/manual and Activ GP/manual groups with respect to residual material in the total canal area (P<0.05). There were no significant differences between manual and ProTaper groups. When using gross radiographic criteria, the Activ GP was more effectively removed from root canals than AH Plus with hand instrumentation. Hybrid Root SEAL, EndoSequence BC Sealer and AH Plus were removed to a similar extent. ProTaper Universal retreatment instruments were as safe and effective as hand instruments in reaching the working length.